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Sample GSM4100950 Query DataSets for GSM4100950
Status Public on Jan 14, 2021
Title 14224X3 HC494P
Sample type SRA
 
Source name pancreas
Organism Mus musculus
Characteristics strain: mixed 129/B6
genotype: Hnf4a F/F
Extracted molecule total RNA
Extraction protocol miRNAeasy kit (Qiagen)
TruSeq Stranded RNA kit with Ribo-Zero Gold (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 92.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2.
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).
 
Submission date Sep 30, 2019
Last update date May 16, 2022
Contact name Eric Snyder
E-mail(s) eric.snyder@hci.utah.edu
Organization name University of Utah, Huntsman Cancer Institute
Department Pathology
Street address 2000 Circle of Hope Drive
City Salt Lake City
State/province UT
ZIP/Postal code 84103
Country USA
 
Platform ID GPL17021
Series (2)
GSE138144 Hnf4a regulated transcriptome in murine PDAC autochthonous tumors [FFPE tumors]
GSE138145 Hnf4a regulated transcriptome
Relations
BioSample SAMN12871821
SRA SRX6922462

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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